The number of variant predictions is dwarfed by the number of common variants, segdups, and SSRs to mask. Rather than storing the regions to mask in an interval forest, store the predictions and query the using the regions to mask.
Probably want to add a flag to the variant.annotate() method to overwrite instead of append an INFO value.
The number of variant predictions is dwarfed by the number of common variants, segdups, and SSRs to mask. Rather than storing the regions to mask in an interval forest, store the predictions and query the using the regions to mask.
Probably want to add a flag to the
variant.annotate()
method to overwrite instead of append an INFO value.